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Relaxation of constraint (Read 2537 times)

ofedrigo

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Relaxation of constraint
Mar 2^nd, 2010 at 7:57am

Does anyone know a test for testing for lineage specific relaxation of constraint (not positive selection)?
What do you think about using the improved branch-site model (Zhang et al., 2005) and if the alternative model is rejected, looking at the fraction of sites under constraint relaxation estimated by the null model? it seems clumsy to me, but I can't think about another way...

Thanks,

Olivier

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Sergei

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Re: Relaxation of constraint
Reply #1 - Mar 2^nd, 2010 at 3:28pm

Hi Olivier,

I am not a big fan of that particular model (see the attached for the reason why), but I would concur with your assessment that there are no particularly good models to test for this. In fact, what IS relaxation of constraint? Is it merely that the mean dN/dS along a branch is between the [0,1), negatively selected tree average and 1?

Cheers,
Sergei

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ofedrigo YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 14	Re: Relaxation of constraint Reply #2 - Mar 2^nd, 2010 at 4:25pm Sergei, Thanks for the pdf. This is a very clear and convincing article. Olivier
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